R Notebook

library(kableExtra)

Attaching package: ‘kableExtra’

The following object is masked from ‘package:dplyr’:

    group_rows

markers <- read.table('output/markergenes/180831/markers_10x-180831_upperbranch_lowerbranch_negbinom.tsv', header=T)

cannot open file 'output/markergenes/180831/markers_10x-180831_upperbranch_lowerbranch_negbinom.tsv': No such file or directoryError in file(file, "rt") : cannot open the connection

U branch marker genes all wolfrum data

markers_u <- markers[markers$avg_logFC > 0,]
markers_u <- markers_u[order(-markers_u$avg_logFC),]

Top 80 markers for metabolic branch sorted on logFC.

for(i in 1:length(plots)) {
  plots_edited[[i]] <- plots[[i]] + NoAxes()
  save_plot(paste('/projects/pytrik/sc_adipose/analyze_10x_fluidigm/10x-adipocyte-analysis/figures/figures_paper/supplementary_figures/wolfrum/u_l_branch_markers/all_data/U_branch/', as.vector(markers_u$gene[i]) ,'.pdf', sep=''), plots_edited[[i]], base_height=6, base_width=6)
}

grid_2

L branch marker genes all wolfrum data

markers_ecm <- markers[markers$avg_logFC < 0,]
markers_ecm <- markers_ecm[order(markers_ecm$avg_logFC),]
kable(markers_ecm) %>%
  kable_styling(bootstrap_options = "striped", full_width = F)

Top 60 ECM branch genes sorted on logFC.

grid_ecm